https://cgi.duke.edu/web/sciwriting/index.php?action=passive_voice

Passive Voice in Scientific Writing

Few topics engender such heated debates as that of active vs. passive voice. This argument is relevant to writing in general, but I think it's particularly so to scientific writing. Some writers speak out in vehement opposition to passive voice, others claim it should be used liberally. What is one to do?

Everyone will have to make his own decision. I think the most important thing is that you've thought about it and you make the decision consciously. At the risk adding to an already saturated debate, I'll present my opinion in hopes that this summary of the issues will be useful. I hope this will help you reach your own conclusion.

As usual, I think the right answer lies somewhere between the extremes. It's true that active voice is generally shorter and clearer, but passive voice is also useful. If I sound like I'm generally on the side of preferring active voice where possible, it's because I believe many scientists habitually abuse the passive voice. The problem isn't with the passive voice per se, it's that scientists don't use it well.

Here's a list of articles I've found over the years that address the debate particular to scientific writing. There are many more articles arguing against passive voice than for it; this might be partially my bias. The articles that argue for the passive voice are usually suggesting certain, limited use cases. After the list of articles you'll find my summary of arguments in both directions, along with my opinion as to whether or not the arguments have merit.

Articles arguing against the passive

Title	Author	Source
Passive Voice (Science editorial)	R.V. Ormes	Science, 1957
Passive Voice and Personal Pronouns (Science letter)	Jane J. Robinson	Science, 1957
Instructions for Contributors (Science)	Editors of Science	Science, 1963
That pernicious passive voice	J Kirkman	Physics in Technology, 1975
How we write about biology	Randy Moore	The American Biology Teacher, 1991
Write to Reply (Nature correspondence)	Leon Avery	Nature, 1996
Passive voice (Nature correspondence)	Alan M. Perlman	Nature, 1996
Writing a clear and engaging paper for all astronomers	Leslie Sage	2003
Are we active? Or should the passive be used?	Rupert Sheldrake	School Science Review, 2004
Writing intelligible English prose for biomedical journals	John Ludbrook	Clinical and Experimental Pharm. and Phys., 2007
What does scientific language prove?	Elise Langdon-Neuner	Journal of the European Medical Writers Association, 2007
How to write (Nature style guide)	Nature editors	Nature, 2011

Most scientists use passive voice either out of habit or to make themselves seem scholarly, objective or sophisticated. Scientists have not always written in passive voice. First-person pronouns such as I and we began to disappear from scientific writing in the United States in the 1920s when active voice was replaced by today's inflexible, impersonal and often boring style of scientific writing. (Randy Moore, editor, The American biology teacher,here).

Articles defending or encouraging the passive

Title	Author	Source
Passive Voice (Science editorial)	R.V. Ormes	Science, 1957
Passive Voice and Personal Pronouns (Science letter)	Jane J. Robinson	Science, 1957
The Science of Scientific Writing	George Gopen and Judith Swan	American Scientist, 1990
The case for the passive voice (Nature correspondence)	Simon R. Leather	Nature, 1996
Clear as Mud (Nature news)	Jonathan Knight	Nature, 2003
Using the Passive Voice in Scientific Writing	Charlene Sorenson and Tonya Johnson	Gallaudet University Web Page, 2004-2011

Arguments for the active

To start with, lets consider all the arguments that can be made for the active voice.

1. Length

Active voice is shorter than passive voice (usually only slightly). It's hard to argue with this one. It may not seem important to you, but if you can write more concisely, you should.

2. Dangling modifiers

Our chief objection to the passive voice is that it sometimes seems to make authors forget to watch for dangling modifiers. Such oversights can lead to something more undesirable than lack of grammatical exactness; they can also lead to scientific inexactness.

If you aren't already familiar with why this is, read a bit more about dangling modifiers. If you're careful, you can use passive and avoid dangling modifiers, but it takes discipline that many lack.

3. Passive sounds pompous or impersonal

"The test tube was carefully smelled." I was astonished to read this sentence in my 11-year-old son's science notebook. At primary school his science reports had been lively and vivid. But when he moved to secondary school they became stilted and artificial. -Rupert Sheldrake

Writing can be pompous in either active or passive voice; impersonality is definitely more the purview of the passive.

4. Passive voice leads to ambiguous actors

One of the key problems with passive voice is that it is easy to leave actor ambiguity. It may be the case that the actor is completely obvious, in which case it is fine to leave her out. However, in many cases, it's not so easy to figure out, and if you leave out the actor, your reader may get it wrong.

5. Passive voice encourages nominalizations

A major problem with passive is that it makes it easier to use abusive nominalizations. I'll assume you've been through the lesson that discusses nominalizations (lesson 1)...if not, go read that first!

I've read lots of papers with some variation of the phrase "the DNA was then subjected to qPCR analysis" or something like that. I rarely read the active counterpart, "we subjected the DNA to qPCR analysis". Somehow the first (which is even worse than the second) seems acceptable. The main problem with this sentence isn't that it's passive, it's that it has nominalized the action of the sentence into "qPCR analysis." As such, you can fix the problem by fixing the nominalization while retaining the passive: "the DNA was then analyzed using qPCR." Nevertheless, somehow awkward phrases like these seem more abundant in passive sentences.

J Kirkman summarizes this argument fantastically:

If we accept the premise that all scientific papers must be passive and impersonal, inevitably we find ourselves tempted to use these 'carrier verbs'. If we will not write:
'we sampled the ions from the plasma by'
'I removed the coating with alcohol'
'we did not inspect the burners regularly'

we can write in simple passive form:
'the ions from the plasma were sampled by'
'the coating was removed with alcohol'
'the burners were not inspected regularly'.

But it is tempting to take a further step and expand these statements to:
'ion sampling from the plasma was achieved by'
'removal of the coating was effected by the application of alcohol'
'regular inspections of the burners were not carried out'.

In taking this extra step we not only change the verb forms from active to passive, but also introduce colourless 'general purpose' verbs 'carrying' abstract nouns. We no longer sample, remove and inspect; we achieve, effect and carry out. -J Kirkman

This is a serious, serious problem in scientific writing.

6. Active is more direct and clear

This argument is a summary of 3 of the preceding arguments: dangling modifiers, ambiguous subjects, and abusive nominalizations. These three things contribute to confusion often associated with passive voice. Accordingly, it's possible to write direct and clear passive sentences. It's just harder.

[Passive voice,] when used correctly can generate as much passion and stimulation as the skilled use of the active voice. -Simon R. Leather

Since I believe it's difficult for most writers to use it "correctly," this argument still holds.

7. Active voice appropriately describes science, which is actively done by scientists.

A matter of opinion -- which camp do you belong to? The "scientists are an integral part of the research" camp, or the "remove the actor to increase objectivity" camp? I subscribe to the former, but maybe this ends in an opinion.

After all, human agents are responsible for designing experiments...writing awkward phrases to avoid admitting their responsibility and their presence is an odd way of being objective. -Jane J. Robinson

8. Journals prefer active voice

It may not have always been this way, but currently, the survey says:

Nature journals like authors to write in the active voice ("we performed the experiment..." ) as experience has shown that readers find concepts and results to be conveyed more clearly if written directly. Nature

Choose the active voice more often than you choose the passive, for the passive voice usually requires more words and often obscures the agent of action. Use first person, not third; do not use first person plural when singular is appropriate. Science, vol. 141 here).

Arguments for the passive

1. Passive stresses what was done

It makes sense to use passive to stress what was done if that is the purpose of the writing. However, it must always be clear who the actor was. Sometimes I find that using the passive voice in the methods section leaves ambiguity. Personally, I find it easier to read active methods sections because I never wonder who did what. Not everyone agrees that it is appropriate to remove actors in order to stress the action:

Passive voice is usually unconvincing because it suggests that scientists were acted upon rather than that scientists acted. - Randy Moore

2. Active leads to personal pronouns

But what's wrong with personal pronouns? Some scientists overuse passive because they are reluctant to use first-person pronouns (we or I). I do not share this reluctance, and neither did Watson and Crick.

Expressions such as 'was performed', 'were conducted', 'were experienced', 'were carried out', 'was achieved', 'was shown', 'were effected', 'were observed', 'resulted' and 'occurred' are desperately overworked in scientific writing because scientists are reluctant to write directly and personally... So the writer who wants to say 'We calculated the yield and found that' pauses, and contorts his thought into the clumsier expression 'Calculations of the yield were performed which revealed that'. -J Kirkman

The hackneyed argument against using personal pronouns revolves around samples of writing that begin every sentence with "We...", and, accordingly, sound terrible. That problem is not with active voice, it's with the repetitive writing style.

3. Passive is more objective and scientific

Some people claim that passive voice is inherently more scientific than active voice:

[T]he use of the passive voice encourages precision and probity. -Simon R. Leather

Why use passive voice? 1. Let the facts stand on their own! 2. Removes some accusations of bias (who did it, how many did it.) 3. Presents an "air" or feeling of logic. -Gallaudet University English Department

I suppose this argument comes down to opinion; I agree with these editors:

Validity of results remains the same regardless of whether they are reported in the active or passive voice. -Elise Langdon-Neuner

Objectivity is a personal trait unrelated to writing - Randy Moore

[W]riters should write naturally and economically, without affectation of a special 'scientific style'. -J Kirkman

4. Passive voice provides structure control

The passive is not only acceptable but a necessary tool if a writer is to have complete control over the structuring of sentences. (George Gopen, Expectations, p. 17).

With this argument I wholeheartedly agree. The key use of passive voice is to switch the order of the subject and object. It is important to have the correct backwards-linking information at the beginning of the sentence. This may require passive voice.

Conclusion

Generally, I prefer active voice, but I think the passive voice has its place in scientific writing. The best thing to do is use a mix of the two. Use passive when necessary to maintain cohesion. When you do, make sure the actor is not ambiguous, be careful to check for dangling modifiers, and avoid abusive nominalizations. Make sure your passive sentences are intentional and not habitual. More important than the active vs. passive debate is the structure of your writing. Make your writing flow, connecting one sentence to the next, and it will be understandable.

Comments on the passive voice from Nature - three letters.

1. From Leon Avery

Department of Biochemistry.

University of Texas

Nature 379:293 23Jan1996

SIR -In John Maddox's parting leading article (Nature 378, 521-533; 1995), he repeats a theme often sounded before: that scientists are poor writers (or at least that scientific papers are poorly written), and speculates on the reasons. One reason is that we are forced by our colleagues to write obscurely. This is never mentioned in the endless discussions about scientific writing, but it is true nonetheless.

For instance, Strunk and White advise writers, "Use the active voice". Robert Day adds, "Do not be afraid to name the agent of the action in a sentence, even when it is '1' or 'we'". Following their advice provoked this response from a referee: "Most of my comments concern writing style. My biggest preoccupation with style is that the paper is written in the first person. This should be avoided whenever possible."

Here is some more advice given to authors: "Every scientist should avoid jargon" (Day). "Shortness is a merit in words" (Fowler). "Avoid fancy words" (Strunk and White). But scientists who have followed it know that their colleagues don't agree. The word "get" in their manuscripts is crossed out and replaced with "obtain" (occasionally with the comment "colloquial" in the margin). "Use" becomes utilize, "method" becomes (usually incorrectly) "methodology", and so on.

The worst sin is liveliness of style. Many scientists are earthy in speech but can't distinguish dignity from pomposity in prose. Lively writing will usually provoke criticism. If you attempt to include an actual JOKE in a scientific paper, you have a major fight on your hands.

Peer pressure can't completely explain why scientific writing has become so dark and dull. One has still to explain how we scientists picked up this dismal habit. But peer pressure can explain why the habit persists. A young scientist who tries to write well gets stamped on. To avoid the risk of inflaming a referee and having a paper rejected, he desists. In time, the belief that "get" is a colloquialism so grows on him that he automatically crosses it out whenever he sees it.

2. From Simon R. Leather

Department of Biology. Imperial College.

Silwood Park. Ascot

Nature 381:467 6June1996

SIR - Maddox's article accusing scientists of being poor writers engendered a reply from one of the growing number of adherents to the use of the active voice in scientific writing. This practice appears to have arisen in the United States over the past 20 years or so and is now encouraged by authors of otherwise excellent texts on scientific writing, Day for example. It is claimed that the use of the active voice encourages clearer and more exciting writing and that the use of the passive voice is more difficult for the reader and is an expression of false modesty. The truth is that both the teaching of the English language and the standards expected of students have declined from the previous high standards upheld by educators in the English-speaking world. Simply put, the writing of precise prose in the passive voice has become too difficult for many of today's scientists. This is unfortunate for a number of reasons.

Using the passive voice in scientific writing allows the researcher to stand at a distance from his or her work. By standing at a distance, an unbiased viewpoint is much more likely to be reached. An unbiased viewpoint encourages a world view and an open mind, surely prerequisites for good science. Many scientific papers published today refer only to literature published in the past 5 years (in other words, easily located using one of the computer databases available ), are parochial in nature and in many cases put forward old arguments as new. John Lawton terms this habit 'reinventing the wheel' and implies a 30-year cycle.

The use of the passive voice encourages disciplined writing, cases must agree, tenses must be used correctly. It is therefore more demanding, but the precision and professionalism displayed is worth the effort. It is possible to be enthusiastic and to write stimulating and exciting prose using the passive voice. How many of the most memorable prose passages in English literature are written in the active voice?

Using the active voice is an easy option. There is no need to discipline one's thoughts. An author can just pour out his or her thoughts. This leads to careless presentation, particularly in methods and materials sections. As any editor knows, many papers submitted for publication appear to be first, or at the best second, drafts. Most authors using the active voice show no consistency of use. Papers alternate between passive-voice statements and active-voice statements, sometimes in the same paragraph, with no logic for the change of voice. This results in a paper full of inconsistencies and, of course, a general mixture of styles.

Using the active voice engenders possessiveness in the results and/or work. By engendering possessiveness an author risks adopting a biased and partisan stance. Wearing blinkers is no way to conduct good science. The active voice, with its less professional approach and tendency to foster the use of colloquialisms ("hassle" is one example I came across in a submitted manuscript) can make the writing appear quaint and amateur and akin to the offerings seen in amateur journals of natural history .

It is tempting when writing from a partisan viewpoint to descend to spite and denigration of other work. This too often manifests itself in biased and anonymous peer review of manuscripts and grants;. There is also the possibility that use of the active voice and the resulting adoption of results and hypotheses as the author's own personal property lead to an unwillingness to see those results contradicted or refuted. This may, in the worst-case scenario, lead to the fabrication of results, something seen much more today than 20 years ago when the passive voice was de rigueur, as judged by the number of articles concerning the subject seen recently.

In conclusion, the use of the passive voice encourages precision and probity. And when used correctly can generate as much passion and stimulation as the skilled use of the active voice. The active voice encourages carelessness, partisanship, and as used by many of its adherents, does no favours to the English language or science.

3. From Alan M. Perlman Kraft Foods, Inc.,

Northfield, Illinois 60093, USA

Nature 382:108 11July1996

SIR -I am an academically trained linguist (PhD, University of Chicago). I have spent 14 years teaching English composition and linguistics in various universities, where I have taught graduate: seminars on the structure and process of written language, and 15 more as a professional writer. I am not a regular reader of your publication; my brother, who is, showed me Simon Leather's letter, which purports to make "the case for the passive voice" (Nature 381, 467; 1996).

About all that I can say with certainty regarding the passive voice is that it omits the performer of the action, for reasons that may be: contextual (the reader already knows who or what performed the action, so mentioning the agent is redundant); rhetorical (either the agent is unknown or irrelevant, or the writer wishes to conceal his/her/its identity); structural (the writer wishes to keep sentence-topic consistent from one: sentence to the next); or cultural (as in scientific writing, where use of the passive, rigidly enforced by senior members of the community, serves as a sign of in-group membership).

Leather goes far beyond these simple truths, with absolutely no scientific data. Where are the quantitative stylistic analyses, where is the behavioral or psycholinguistic research to support his statements that "the use of the passive voice encourages disciplined writing" (indeed, tenses must be used correctly" in all writing); that “using the active voice encourages possessiveness in the results and/or work;" that “the active voice [has a] tendency to foster colloquialisms;" that “the use of the active voice leads to an unwillingness to see [the author's] results contradicted" and to "the fabrication of results"? I know of no such research. I strongly doubt that it exists.

I consider Leather's letter an outrageous display of scientific hypocrisy. He makes dogmatic pronouncements on a subject he knows nothing about - It's as if I, armed only with my tenth-grade biology course, were to undertake to prove the superiority of mammals over reptiles, on the grounds that the former are cuddly and smart, whereas the latter are slimy and stupid.

Leather should practice what he preaches: of the 18 transitive sentences in his letter, only four were in the passive. 

ifort and mkl

Install location:
    /opt/intel/composer_xe_2013_sp1.3.174

Component(s) selected:
    Intel(R) Fortran Compiler XE 14.0 Update 3                             563MB
        Intel Fortran Compiler XE                                              

    Intel(R) Debugger 13.0                                                 477MB
        Intel Debugger                                                         

    Intel(R) Math Kernel Library 11.1 Update 3                             1.9GB
        Intel MKL core libraries                                               
        Intel(R) Xeon Phi(TM) coprocessor support                              
        Fortran 95 interfaces for BLAS and LAPACK                              
        GNU* Compiler Collection support                                       

    GNU* GDB 7.5                                                           119MB
        GNU* GDB 7.5 on Intel(R) 64 (Provided under GNU General Public License 
v3)
        GDB Eclipse* Integration on Intel(R) 64 (Provided under Eclipse Public 
License v.1.0)

Install WEBMO

yum install tcsh
yum install ncompress
yum install gcc
yum install gcc-c++
yum install gcc-gfortran
yum install atlas (Math Lib)
yum install autoconf
yum install libtool
yum install bison
yum install flex
yum install pcre
yum install pcre-devel
yum install perl-CGI
yum install apr
yum install apr-util
yum install httpd
yum install php
service iptables start (must be running before httpd is turned on)
 chkconfig iptables on (did not work; still need to "service iptables star" after reboot)
service httpd start
chkconfig httpd on
/etc/httpd/conf.d> diff userdir.conf userdir.conf.orig
33,41c33,35
<         Options Indexes Includes FollowSymLinks
< 
<         ## Apache 2.4 users use following ##
<           Require all granted
< 
<         ## Apache 2.2 users use following ##
<           AllowOverride All
<           Allow from all
<           Order deny,allow
---
>     AllowOverride FileInfo AuthConfig Limit Indexes
>     Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
>     Require method GET POST OPTIONS


set the hostname straight -- the eburg-##.reg.cwu.edu hostname won't work. Use pc#####.d.cwu.edu

Installation as root:

Get WebMO.14.0.007.tar (License Number in Email)
tar xvf WebMO.14.0.007.tar
cd WebMO.install
perl setup.pl

Here are the configuration options that you have chosen
License number:       ...
Path to perl:         /usr/bin/perl
Webserver name:       eburg-10.reg.cwu.edu
HTML directory:       /var/www/html/webmo
HTML URL:             /webmo
CGI script directory: /var/www/cgi-bin/webmo
CGI script URL:       /cgi-bin/webmo
User files directory: /var/webmo

Once WEBMO is installed, the login URL is
http://hostname/cgi-bin/webmo/login.cgi

username: admin
password: blank

change password after login. Set up new users with passwords.

Now GAMESS:

Put GAMESS under the webmo prefered /usr/local/gamess
./config
(choose gfortran and atlas both are freely available for Fedora 20)
The actvte.code will be automatically modified, compiled, and executed.

When doing lked, ld may not be able to find -latlas and -lf77blas because in the /usr/lib64/atlas folder these two library's names contains version numbers that need to be removed:

cd /usr/lib64/atlas
sudo ln -s libatlas.so.3.0 libatlas.so
sudo ln -s libf77blas.so.3.0 libf77blas.so

cp -r /home/yingbin/gamess /usr/local/gamess (default directory of WEBMO)

cd /var/www/cgi-bin/webmo
vi run_gamess.cgi
add "$ENV{'ERICFMT'} = "/home/yingbin/gamess/ericfmt.dat";" and other environmental variables if needed.

Installation as regular
[webmo@pc##### webmo]$ diff run_gamess.cgi run_gamess.cgi.orig
70d69
< $ENV{'ERICFMT'}="/home/yingbin/gamess/ericfmt.dat";

Installation of Fedora 20 (64 bit)

1. Download Fedora-20-x86_64-DVD.iso (4.3 GB).

https://fedoraproject.org/en_GB/download-splash?file=http://download.fedoraproject.org/pub/fedora/linux/releases/20/Fedora/x86_64/iso/Fedora-20-x86_64-DVD.iso

2. Burn the iso file to a DVD (I used BurnAware).

3. Insert the DVD, connect the computer to Ethernet jack, restart the computer. Mine is Dell PowerEdge 1950 with one quad-core processor (2.5GHz).

4. Press F11 to enter the boot device menu. Choose "IDE CD-ROM device." IDE stands for "Integrated Drive Electronics."

5. Set  the  hostname to be pc#####.d.cwu.edu.

6. I decides to erase all previous data and system files. Click "Installation Destination."
The partition for the slave nodes:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830 (8GB should be enough. 16GB just in case)
/:  412.73 GB LVM, ext4, fedora_pc89830

The partition for the master node:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830
/home:  100 GB LVM, ext4, fedora_pc89830
/:  312.73 GB LVM, ext4, fedora_pc89830

The partition for the web server:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830
/var:  300 GB LVM, ext4, fedora_pc89830 (webmo, etc)
/:  112.73 GB LVM, ext4, fedora_pc89830

7. The installation will start and take ~30 minutes. During which you may take time to set password for root and set up a local user account (for yourself).

8. p1p1 connected  to the internet. em1 and em2 (192.168.2.1?[1-2]) to the switch.  Open Firefox to register the computer (CWU policy). The hardware address is the MAC address of the network interface card (or NIC, network interface controller, network adapter, LAN adapter) connected to the Internet.

9. If you have several network cards like I do, only one will be connected on reboot by default. To enable all NICs, open a terminal, "cd /etc/sysconfig/network-scripts", "vi ifcfg-*", then replace every "ONBOOT=no" to "ONBOOT=yes". It is optional to enclose "yes" with double quotes. Note that p1p1 may not  connect to the internet until ifdown em1 and ifdown em2.

10. Then run "shutdown -P now" to power off the computer and wait for 5 minutes (CWU procedures) before turning on the computer. Again the computer should be connected to the Internet. Run "ifconfig" to see all NIC information including their 48-bit MAC (media access control) address.

11. Install tcsh and ncompress on all nodes. Then gcc, gfortran, and whatever is needed on  the master node.

12. "service iptables start/stop" to turn on/off the Firewall. "chkconfig iptables on/off" to turn on/off the firewall on reboot.

13. vi /etc/host* to edit hostnames, allowed and denied ones. Do NOT rush setting denied hostnames using regular expressions; this may block computers you want to connect to the server.

14. Install clamav. SELINUX must be disabled for the ifort installation. "cat /etc/selinux/config" to view the file.

15. yum install gcc-c++ (g++ is needed for ifort installation)  yum install libstdc++.so.5 before the installation of ifort and mkl.

How to clean up semaphores

A. Identify all semaphores

ipcs -a

------ Shared Memory Segments --------
key        shmid      owner      perms      bytes      nattch     status     
0x00000000 9043975    yingbin    600        160525768  1          dest        
0x00000000 9306129    yingbin    600        160525768  1          dest        
0x00000000 9076754    yingbin    600        160525768  1          dest        

------ Semaphore Arrays --------
key        semid      owner      perms      nsems    
0x00000000 17924096   yingbin    600        25       
0x00000000 17956865   yingbin    600        25       
0x00000000 17989634   yingbin    600        1        
0x00000000 17137682   yingbin    600        25       
0x00000000 17170451   yingbin    600        25       
0x00000000 17203220   yingbin    600        1        
0x00000000 17235992   yingbin    600        25       
0x00000000 17268761   yingbin    600        25       
0x00000000 17301530   yingbin    600        1        

------ Message Queues --------
key        msqid      owner      perms      used-bytes   messages   

B. Identify the process ID (pid) that are associated with the semaphores

 ipcs -s -i 17301530

Semaphore Array semid=17301530
uid=1005         gid=100         cuid=1005       cgid=100
mode=0600, access_perms=0600
nsems = 1
otime = Mon Apr  7 09:27:24 2014 
ctime = Mon Apr  7 09:27:24 2014 
semnum     value      ncount     zcount     pid      
0                1000              0          0          27036    

C. Find if the process 27036 is still active or has been killed.

ps -ef |grep 27036


D. If the process has been killed, the associated semaphores can be safely cleaned.

ipcrm -s 17301530

Reaction rate constants for the uni-, bi-, and tri-molecular reactions

Eyring equation: k = (kBT/h) e^(-delta G/RT)

The above equation can be use for uni-molecular directly. The simplified interpretation is that the reaction rate constant is proportional to the frequency of the reaction mode (kBT/h) and the relative concentrations of the transition state and the reactant(s):
[P(TS)/1 bar] / [P(reactant)/1 bar] = e^(-delta G/RT), where delta G is the standard Gibbs energy difference between the transition state and the reactant at temperature T and the standard state.

For a bi-molecular reaction, [P(TS)/1 bar] / {[P(A)/1 bar][P(B)/1 bar]} = e^(-delta G/RT),and again, the delta G is the standard Gibbs energy difference between the transition state and the two reactants at temperature T and the standard state..

For the bi- and tri-molecular reactions, we have learned that the reaction rate constants should be s^(-1)M^(-1) and s^(-1)M^(-2). Why? And how can we still use the Eyring equation to obtain the reaction rate constant given the Gibbs energy of activation?

Note that delta G refers to the difference between the STANDARD Gibbs energy of the transitions state (TS) and that of the reactant(s). The STANDARD state for gases is 1 bar!

Therefore, the Eyring equation can still be used to calculate the rate constant k for the bi- and tri-molecular reactions as long as we use PRESSURE/(1 bar) consistently in the expression of the reaction rate.

For example, A + B -> C

Reaction rate = d[P(C)/1 bar)]/dt = -d[P(A)/1 bar)]/dt = -d[P(B)/1 bar)]/dt = k[P(A)/1 bar)][P(B)/1 bar)]

Note that [P(A)/1 bar)], [P(B)/1 bar)], [P(C)/1 bar)] are unit-less. Pressures are divided by 1 bar because the delta G are usually determined at 1 bar. GAMESS calculations also give the values of delta G at 1 bar by default.

Therefore, we can see the left-hand-side (lhs) of the equation is in s^(-1) and so is the rhs.

d[P(C)/1 bar)]/dt = k[P(A)/1 bar)][P(B)/1 bar)]

What if the users of the above equation prefer to use M (mol/L)?
 Again, we can simply derive the equation in terms of concentrations.

d[P(C)/1 bar)]/dt = k[P(A)/1 bar)][P(B)/1 bar)]

d([C]RT/1 bar)/dt = k ([A]RT/1 bar) ([B]RT/1 bar)

 d([C])/dt = k(RT/1 bar) [A] [B]

Therefore the rate constant of a bi-molecular reaction becomes the product of 3 terms:
 the rate constant in s^(-1)M^(-1) = (kBT/h) e^(-delta G/RT) (RT/1 bar)

For a tri-molecular reaction, the rate constant = (kBT/h) e^(-delta G/RT) (RT/1 bar)^2 

Note that many rate constants of bi-molecular reactions are in the units of (s, cm, molecule),
We simply need to find the value of (RT/1 bar) in (s, cm, molecule)
 
For example, at 298.15K,
(RT/1 bar) = (8.3145 * 298.15) / 100000 = 0.024790 m^3/mol = 4.1164 * 10^(-20) cm^3/molecule

T(K) kB T/p (cm^3/molecule) 100 1.38065E-20 200 2.76130E-20 298.15 4.11641E-20 300 4.14195E-20 400 5.52260E-20 500 6.90325E-20 600 8.28390E-20 700 9.66455E-20 800 1.10452E-19 900 1.24259E-19 1000 1.38065E-19 1100 1.51872E-19 1200 1.65678E-19 1300 1.79485E-19 1400 1.93291E-19 1500 2.07098E-19 1600 2.20904E-19 1700 2.34711E-19 1800 2.48517E-19 1900 2.62324E-19 2000 2.76130E-19 2100 2.89937E-19 2200 3.03743E-19 2300 3.17550E-19 2400 3.31356E-19 2500 3.45163E-19

Numerical Hessian for a plannar molecule with n atoms

n atoms:(x1, y1, 0), (x2, y2, 0), (x3, y3, 0), ...

A total of (1 + 9*n^2) energy calculations need to be performed:

1: at equilibrium geometry.
n*1: for 1z-1z 2z-2z,3z-3z,....
[n*(n-1)/2]*2: for 1z-2z, 1z-3z, 1z-4z, 2z-3z, 2z-4z, 3z-4z.
[(2n)^2]*4/2: for the second derivatives with respect to x(s) and y(s)

1 + n + n*(n-1) + 8*n^2 = 1 + 9*n^2

For example, Numerical Hessian for a plannar molecule with 3 atoms

3 atoms:(x1, y1, 0),(x2, y2, 0),(x3, y3, 0)

82 energy calculations need to be performed:

1: at equilibrium geometry.
3: for 1z-1z 2z-2z,3z-3z
3*2: for 1z-2z, 1z-3z, 2z-3z.
2*6^2: for the second derivatives with respect to x(s) and y(s)

1 + 3 + 6 + 72 = 82 (verified by an AM1 method=fullnum Hessian calculation on HOCl)

For a planar molecule such as trans-HNOH with 4 atoms, 1+9*4^2=145 energy calculations need to be carried out to obtain the numerical Hessian.

 $force temp(1) = 1100.00, 1200.00, 1300.00, 1400.00, 1500.00,
                  1600.00, 1700.00, 1800.00, 1900.00, 2000.00
  method=fullnum projct=.t.
 $end
 $contrl maxit=200 mult=2 scftyp=uhf runtyp=hessian coord=unique $end
 $basis gbasis=am1 $end
 $system timlim=1000000 mwords=80 $end
 $data
 HNOH
 Cs

 O           8.0   0.0094634591  -0.0934516366   0.0000000000
 N           7.0   1.2729078083   0.1027207551   0.0000000000
 H           1.0  -0.4112060327   0.7952578868   0.0000000000
 H           1.0   1.7288347653  -0.8045270053   0.0000000000
 $end

For a non-planar  molecule with 4 atoms, see the post on H2NO.